SMTL ID : 9clq.1

PANK3 complex structure with compound PZ-4352

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x 01: 2-(4-cyclopropyl-2-fluorophenyl)-1-[4-(6-fluoro[1,3]oxazolo[4,5-b]pyridin-2-yl)piperazin-1-yl]ethan-1-one

01.1: 21 residues within 4Å: Chain A: V.202, S.203, R.215, T.217, G.218, T.219 Chain B: V.258, I.261, Y.262, L.271, V.276, A.277, N.307, G.310, S.311, R.314, A.345, L.346, W.349 Ligands: EDO.3, ANP.6 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.261, B:Y.262, B:L.271, B:A.277, B:A.345 Hydrogen bonds: B:R.314, A:R.215, A:R.215 pi-Stacking: B:W.349 pi-Cation interactions: A:R.215 01.8: 21 residues within 4Å: Chain A: V.258, I.261, Y.262, L.271, V.276, A.277, N.307, G.310, S.311, R.314, A.345, L.346, W.349 Chain B: V.202, S.203, R.215, T.217, G.218, T.219 Ligands: EDO.10, ANP.13 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:I.261, A:Y.262, A:L.271, A:A.277, A:A.345 Hydrogen bonds: A:R.314, B:R.215, B:R.215 pi-Stacking: A:W.349 pi-Cation interactions: B:R.215

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 8 residues within 4Å: Chain A: D.25, L.150, N.197, E.362, G.363, Y.364, F.365, G.366 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.365 Hydrogen bonds: A:D.25, A:N.197, A:E.362, A:F.365, A:G.366 Water bridges: A:E.146, A:A.367 ACT.9: 8 residues within 4Å: Chain B: D.25, L.150, N.197, E.362, G.363, Y.364, F.365, G.366 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.365 Hydrogen bonds: B:N.197, B:E.362, B:F.365, B:G.366 Water bridges: B:A.367

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 10 residues within 4Å: Chain A: E.146, N.197, G.199, S.200, G.201, V.202, S.203 Ligands: 01.1, ANP.6, MG.7 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.146, A:G.199, A:G.201, A:G.201, A:S.203 Water bridges: A:E.146, A:N.197 EDO.4: 7 residues within 4Å: Chain A: L.30, T.69, I.71, R.94, F.95, P.96 Ligands: ANP.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.94 EDO.5: 6 residues within 4Å: Chain A: L.227, S.231, C.236, E.237 Chain B: I.284, R.289 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.289, B:R.289 Water bridges: B:K.286 EDO.10: 10 residues within 4Å: Chain B: E.146, N.197, G.199, S.200, G.201, V.202, S.203 Ligands: 01.8, ANP.13, MG.14 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.146, B:G.199, B:G.201, B:G.201, B:S.203 Water bridges: B:N.197, B:N.197 EDO.11: 7 residues within 4Å: Chain B: L.30, T.69, I.71, R.94, F.95, P.96 Ligands: ANP.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.94 EDO.12: 6 residues within 4Å: Chain A: I.284, R.289 Chain B: L.227, S.231, C.236, E.237 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.289, A:R.289 Water bridges: A:K.286

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.6: 22 residues within 4Å: Chain A: G.27, G.28, T.29, L.30, K.32, I.198, G.199, S.200, G.201, G.223, G.224, F.239, E.240, G.329, N.330, F.331, R.333 Chain B: I.261 Ligands: 01.1, EDO.3, EDO.4, MG.7 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:G.28, A:T.29, A:L.30, A:L.30, A:K.32, A:R.94, A:G.199, A:S.200, A:S.200, A:G.201, A:G.223, A:E.240, A:N.330, A:N.330, A:F.331, A:R.333 Water bridges: A:K.32, A:K.32, A:E.146, A:E.146, A:E.146, A:N.197, A:N.197 Salt bridges: A:K.32 pi-Stacking: A:F.239 ANP.13: 22 residues within 4Å: Chain A: I.261 Chain B: G.27, G.28, T.29, L.30, K.32, I.198, G.199, S.200, G.201, G.223, G.224, F.239, E.240, G.329, N.330, F.331, R.333 Ligands: 01.8, EDO.10, EDO.11, MG.14 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:G.28, B:T.29, B:L.30, B:L.30, B:K.32, B:R.94, B:G.199, B:S.200, B:S.200, B:G.201, B:G.223, B:E.240, B:N.330, B:N.330, B:F.331, B:R.333 Water bridges: B:T.29, B:K.32, B:K.32, B:N.197, B:N.197 Salt bridges: B:K.32 pi-Stacking: B:F.239

2 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 3 residues within 4Å: Chain A: K.32 Ligands: EDO.3, ANP.6 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain B: K.32 Ligands: EDO.10, ANP.13 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yun, M. et al., PANK3 complex structure with compound PZ-4352. To Be Published

Release Date

2025-07-16

Peptides

Pantothenate kinase 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Pantothenate kinase 3

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